Fix output bug

biointec · Mar 2, 2016 · 6738d1a · 6738d1a
1 parent a26d6a1
commit 6738d1a
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 4 deletions.
diff --git a/src/AlignedRead.cpp b/src/AlignedRead.cpp
@@ -140,7 +140,7 @@ std::string AlignedRead::getCorrectedRead(Graph const &graph) {
 	}
 	int max_cov = 0;
 	LocalAlignment best_la;
-	for (auto la : local_alignments_) {
+	for (auto &la : local_alignments_) {
 		int cov = la.get_read_end() - la.get_read_start();
 		if (cov > max_cov) {
 			max_cov = cov;

diff --git a/src/ReadCorrection.cpp b/src/ReadCorrection.cpp
@@ -12,7 +12,7 @@ void ReadCorrection::correctRead(ReadRecord& record)
         Alignment alignment(250, 30, 1, -4, -2, -3);
         InterNodeChain iernc(read, graph_, settings_, alignment);
         AlignedRead ar(read, settings_.get_output_mode());
-        record.read = iernc.chainSeeds(ar);
+        record.correction = iernc.chainSeeds(ar);
 }
 
 void ReadCorrection::correctChunk(vector<ReadRecord>& readChunk)

diff --git a/src/library.cpp b/src/library.cpp
@@ -397,9 +397,9 @@ void LibraryContainer::outputThreadLibrary(ReadLibrary& input)
                 // write the idle read buffer (only this thread has access)
                 for (size_t i = 0; i < idlOutputBuffer->size(); i++)
                         if ((*idlOutputBuffer)[i].correction.length() > 0) {
-                                readFile->writeRecord((*idlOutputBuffer)[i]);
+                                readFile->writeCorrectedRecord((*idlOutputBuffer)[i]);
                         } else {
-                                uncorrectedFile->writeRecord((*idlOutputBuffer)[i]);
+                                uncorrectedFile->writeUncorrectedRecord((*idlOutputBuffer)[i]);
                         }
 
                 if (!readFile->good())

diff --git a/src/readfile/readfile.cpp b/src/readfile/readfile.cpp
@@ -108,3 +108,15 @@ void ReadFile::writeRecord(const ReadRecord& record)
         rfHandler->writeLine(record.read);
         rfHandler->writeLine(record.postRead);
 }
+
+void ReadFile::writeCorrectedRecord(const ReadRecord& record)
+{
+        rfHandler->writeLine(record.preRead);
+        rfHandler->writeLine(record.correction);
+        rfHandler->writeLine(record.postRead);
+}
+
+void ReadFile::writeUncorrectedRecord(const ReadRecord& record)
+{
+        writeRecord(record);
+}
diff --git a/src/readfile/readfile.h b/src/readfile/readfile.h
@@ -466,6 +466,8 @@ class ReadFile {
          * @param record Record to write
          */
         virtual void writeRecord(const ReadRecord& record);
+        virtual void writeCorrectedRecord(const ReadRecord& record);
+        virtual void writeUncorrectedRecord(const ReadRecord& record);
 };
 
 #endif